EST analysis on pig mitochondria reveal novel expression differences between developmental and adult tissues

Karsten Scheibye-Alsing,Merete Fredholm,Jan Gorodkin,Michael J Gilchrist,Susanna Cirera

doi:10.1186/1471-2164-8-367

Karsten Scheibye-Alsing, Merete Fredholm + Show 3 more

Open Access

https://doi.org/10.1186/1471-2164-8-367

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Abstract

BackgroundThe mitochondria are involved in many basic functions in cells of vertebrates, and can be considered the power generator of the cell. Though the mitochondria have been extensively studied there appear to be only few expression studies of mitochondrial genes involving a large number of tissues and developmental stages. Here, we conduct an analysis using the PigEST resource [1] which contains expression information from 35 tissues distributed on one normalized and 97 non-normalized cDNA libraries of which 24 are from developmental stages. The mitochondrial PigEST resource contains 41,499 mitochondrial sequences.ResultsThe mitochondrial EST (Expressed Sequence Tag) sequences were assembled into contigs which covers more than 94 percent of the porcine mitochondrial genome, with an average of 976 EST sequences per nucleotide. This data was converted into expression values for the individual genes in each cDNA library revealing differential expression between genes expressed in cDNA libraries from developmental and adult stages. For the 13 protein coding genes (and several RNA genes), we find one set of six genes, containing all cytochrome oxidases, that are upregulated in developmental tissues, whereas the remaining set of seven genes, containing all ATPases, that are upregulated in adult muscle and brain tissues. Further, the COX I (Cytochrome oxidase subunit one) expression profile differs from that of the remaining genes, which could be explained by a tissue specific cleavage event or degradation pattern, and is especially pronounced in developmental tissues. Finally, as expected cDNA libraries from muscle tissues contain by far the largest amount (up to 20%) of expressed mitochondrial genes.ConclusionOur results present novel insight into differences in mitochondrial gene expression, emphasizing differences between adult and developmental tissues. Our work indicates that there are presently unknown mechanisms which work to customize mitochondrial processes to the specific needs of the cell, illustrated by the different patterns between adult and developmental tissues. Furthermore, our results also provide novel insight into how in-depth sequencing can provide significant information about expression patterns.

Highlights

The mitochondria are involved in many basic functions in cells of vertebrates, and can be considered the power generator of the cell
Differential gene expression To measure the digital expression of specific genes in a given cDNA library, we considered the number of ESTs relative to the library size, which in general, for high confident annotations, has been shown to be in agreement with experimental qPCR results [16]
We investigated 41,499 ESTs which yielded an average coverage of 976 EST per mitochondrial nucleotide position

Summary

Introduction

The mitochondria are involved in many basic functions in cells of vertebrates, and can be considered the power generator of the cell. Though the mitochondria have been extensively studied there appear to be only few expression studies of mitochondrial genes involving a large number of tissues and developmental stages. We conduct an analysis using the PigEST resource [1] which contains expression information from 35 tissues distributed on one normalized and 97 non-normalized cDNA libraries of which 24 are from developmental stages. The mammalian mitochondrion is a system of only few components It consist of 13 protein coding genes, 22 tRNA, two rRNAs and possibly a few non-coding RNAs [2]. The circular mitochondrial genome deviates from the nuclear genome by being extremely compact in nature with almost no inter-spaced non-coding DNA between genes, it has a special codon usage using only the 22 tRNAs to encode the amino acids. The compact nature of the mitochondrion is directly reflected in the transcription mechanism, as all genes are transcribed in polycistronic transcripts which are processed to give the mature RNAs [3,4] (and references therein)

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